Literature summary for 3.1.11.7 extracted from

Tumbale, P.; Schellenberg, M.; Mueller, G.; Fairweather, E.; Watson, M.; Little, J.; Krahn, J.; Waddell, I.; London, R.; Williams, R.
Mechanism of APTX nicked DNA sensing and pleiotropic inactivation in neurodegenerative disease (2018), EMBO J., 37, e98875 .

Cloned(Commentary)

Cloned (Comment)	Organism
recombinant expression of His-tagged human APTX in Escherichia coli strain Rosetta 2 (DE3) cells	Homo sapiens

Crystallization (Commentary)

Crystallization (Comment)	Organism
purified wild-type enzyme in complex with RNA/DNA, hAPTX-nicked-RNA-DNA-AMP-Zn2+ complex is grown by mixing 300 nl of 10 mg/ml hAptx (165-342) protein and 1 mM AMP, 1.5:1 DNA:protein molar ratio, in 150 mM NaCl, 20 mM Tris-HCl, pH 7.5, and 0.1% 2-mercaptoethanol, with an equal volume of precipitant solution containing 100 mM MES, pH 6.5, 16% w/v PEG 3350 at 4°C, methods for mutant product complexes hAPTX-R199H/RNA-DNA/AMP-Zn2+, hAPTXH201Q/RNA-DNA/AMP-Zn2+, hAPTX-S242N/RNA-DNA/AMPZn2+, hAPTX-L248M/DNA/AMP-Zn2+, and hAPTX-V263G/RNA-DNA/AMP-Zn2+, differ, overview. X-ray diffraction structure determination and analysis, molecular replacement using PDB ID 4NDG as a search model	Homo sapiens

Crystallization (Comment)

Organism

purified wild-type enzyme in complex with RNA/DNA, hAPTX-nicked-RNA-DNA-AMP-Zn2+ complex is grown by mixing 300 nl of 10 mg/ml hAptx (165-342) protein and 1 mM AMP, 1.5:1 DNA:protein molar ratio, in 150 mM NaCl, 20 mM Tris-HCl, pH 7.5, and 0.1% 2-mercaptoethanol, with an equal volume of precipitant solution containing 100 mM MES, pH 6.5, 16% w/v PEG 3350 at 4°C, methods for mutant product complexes hAPTX-R199H/RNA-DNA/AMP-Zn2+, hAPTXH201Q/RNA-DNA/AMP-Zn2+, hAPTX-S242N/RNA-DNA/AMPZn2+, hAPTX-L248M/DNA/AMP-Zn2+, and hAPTX-V263G/RNA-DNA/AMP-Zn2+, differ, overview. X-ray diffraction structure determination and analysis, molecular replacement using PDB ID 4NDG as a search model

Homo sapiens

Protein Variants

Protein Variants	Comment	Organism
A198V	site-directed mutagenesis, a mutation causing the neurodegenerative disorder ataxia with oculomotor ataxia 1 (AOA1)	Homo sapiens
A198V/P206L	site-directed mutagenesis, a mutation causing the neurodegenerative disorder ataxia with oculomotor ataxia 1 (AOA1)	Homo sapiens
D185E	site-directed mutagenesis, a mutation causing the neurodegenerative disorder ataxia with oculomotor ataxia 1 (AOA1)	Homo sapiens
D267G	site-directed mutagenesis, a mutation causing the neurodegenerative disorder ataxia with oculomotor ataxia 1 (AOA1)	Homo sapiens
D267G/W279X	site-directed mutagenesis, a mutation causing the neurodegenerative disorder ataxia with oculomotor ataxia 1 (AOA1)	Homo sapiens
G231E	site-directed mutagenesis, a mutation causing the neurodegenerative disorder ataxia with oculomotor ataxia 1 (AOA1)	Homo sapiens
G231E/689insT	site-directed mutagenesis, a mutation causing the neurodegenerative disorder ataxia with oculomotor ataxia 1 (AOA1)	Homo sapiens
H201Q	site-directed mutagenesis, a mutation causing the neurodegenerative disorder ataxia with oculomotor ataxia 1 (AOA1)	Homo sapiens
H201R	site-directed mutagenesis, a mutation causing the neurodegenerative disorder ataxia with oculomotor ataxia 1 (AOA1)	Homo sapiens
K197Q	site-directed mutagenesis, a mutation causing the neurodegenerative disorder ataxia with oculomotor ataxia 1 (AOA1)	Homo sapiens
K197Q/W279X	site-directed mutagenesis, a mutation causing the neurodegenerative disorder ataxia with oculomotor ataxia 1 (AOA1)	Homo sapiens
L223P	site-directed mutagenesis, a mutation causing the neurodegenerative disorder ataxia with oculomotor ataxia 1 (AOA1)	Homo sapiens
L248M	site-directed mutagenesis, a mutation causing the neurodegenerative disorder ataxia with oculomotor ataxia 1 (AOA1)	Homo sapiens
R199H	site-directed mutagenesis, a mutation causing the neurodegenerative disorder ataxia with oculomotor ataxia 1 (AOA1)	Homo sapiens
R247X	site-directed mutagenesis, not involved in AOA1 disease	Homo sapiens
R306X	site-directed mutagenesis, a mutation causing the neurodegenerative disorder ataxia with oculomotor ataxia 1 (AOA1)	Homo sapiens
R306X/W279X	site-directed mutagenesis, a mutation causing the neurodegenerative disorder ataxia with oculomotor ataxia 1 (AOA1)	Homo sapiens
S242N	site-directed mutagenesis, a mutation causing the neurodegenerative disorder ataxia with oculomotor ataxia 1 (AOA1)	Homo sapiens
V263G	site-directed mutagenesis, a mutation causing the neurodegenerative disorder ataxia with oculomotor ataxia 1 (AOA1)	Homo sapiens
V263G/P206L	site-directed mutagenesis, a mutation causing the neurodegenerative disorder ataxia with oculomotor ataxia 1 (AOA1)	Homo sapiens
W279R	site-directed mutagenesis, a mutation causing the neurodegenerative disorder ataxia with oculomotor ataxia 1 (AOA1)	Homo sapiens
W279R/IVS5	site-directed mutagenesis, a mutation causing the neurodegenerative disorder ataxia with oculomotor ataxia 1 (AOA1)	Homo sapiens
W279X	site-directed mutagenesis, a mutation causing the neurodegenerative disorder ataxia with oculomotor ataxia 1 (AOA1)	Homo sapiens
W279X/I159fs	site-directed mutagenesis, a mutation causing the neurodegenerative disorder ataxia with oculomotor ataxia 1 (AOA1)	Homo sapiens
W279X/Q181X	site-directed mutagenesis, a mutation causing the neurodegenerative disorder ataxia with oculomotor ataxia 1 (AOA1)	Homo sapiens
W279X/R306X	site-directed mutagenesis, a mutation causing the neurodegenerative disorder ataxia with oculomotor ataxia 1 (AOA1)	Homo sapiens

KM Value [mM]

KM Value [mM]	KM Value Maximum [mM]	Substrate	Comment	Organism	Structure
0.0000171	-	adenosine-5'-diphospho-5'-[DNA]	nicked DNA substrate, pH 7.5, 25-37°C, recombinant His-tagged wild-type enzyme	Homo sapiens
0.0000371	-	adenosine-5'-diphospho-5'-[DNA]	blunt DNA substrate, pH 7.5, 25-37°C, recombinant His-tagged wild-type enzyme	Homo sapiens

Metals/Ions

Metals/Ions	Comment	Organism	Structure
Zn2+	required	Homo sapiens

Natural Substrates/ Products (Substrates)

Natural Substrates	Organism	Comment (Nat. Sub.)	Natural Products	Comment (Nat. Pro.)	Rev.	Reac.
adenosine-5'-diphospho-5'-[DNA] + H2O	Homo sapiens	-	AMP + phospho-5'-[DNA]	-	?

Organism

Organism	UniProt	Comment	Textmining
Homo sapiens	Q7Z2E3	-	-

Purification (Commentary)

Purification (Comment)	Organism
recombinant His-tagged human APTX from Escherichia coli strain Rosetta 2 (DE3) cells by nickel affinity chromatography	Homo sapiens

Substrates and Products (Substrate)

Substrates	Comment Substrates	Organism	Products	Comment (Products)	Rev.
adenosine-5'-diphospho-5'-[DNA] + H2O	-	Homo sapiens	AMP + phospho-5'-[DNA]	-	?
adenosine-5'-diphospho-5'-[DNA] + H2O	the enzyme can use nicked and blunt substrates	Homo sapiens	AMP + phospho-5'-[DNA]	-	?
additional information	substrate binding structure, overview	Homo sapiens	?	-	?

Synonyms

Synonyms	Comment	Organism
APTX	-	Homo sapiens
RNA-DNA deadenylase	-	Homo sapiens

Temperature Optimum [°C]

Temperature Optimum [°C]	Temperature Optimum Maximum [°C]	Comment	Organism
25	37	assay at	Homo sapiens

Turnover Number [1/s]

Turnover Number Minimum [1/s]	Turnover Number Maximum [1/s]	Substrate	Comment	Organism	Structure
0.38	-	adenosine-5'-diphospho-5'-[DNA]	nicked DNA substrate, pH 7.5, 25-37°C, recombinant His-tagged wild-type enzyme	Homo sapiens
0.51	-	adenosine-5'-diphospho-5'-[DNA]	blunt DNA substrate, pH 7.5, 25-37°C, recombinant His-tagged wild-type enzyme	Homo sapiens

pH Optimum

pH Optimum Minimum	pH Optimum Maximum	Comment	Organism
7.5	-	assay at	Homo sapiens

General Information

General Information	Comment	Organism
malfunction	APTX human mutations cause the neurodegenerative disorder ataxia with oculomotor ataxia 1 (AOA1). AOA1 mutagenic effects on APTX solubility, stability, and catalytic activity, and molecular basis for APTX inactivation in AOA1, APTX mutations variably impact protein folding and activity, overview	Homo sapiens
physiological function	the APTX RNA-DNA deadenylase protects genome integrity and corrects abortive DNA ligation arising during ribonucleotide excision repair and base excision DNA repair, APTX nicked DNA sensing and pleiotropic inactivation in neurodegenerative disease, mechanism	Homo sapiens

kcat/KM [mM/s]

kcat/KM Value [1/mMs^-1]	kcat/KM Value Maximum [1/mMs^-1]	Substrate	Comment	Organism	Structure
13747	-	adenosine-5'-diphospho-5'-[DNA]	blunt DNA substrate, pH 7.5, 25-37°C, recombinant His-tagged wild-type enzyme	Homo sapiens
22222	-	adenosine-5'-diphospho-5'-[DNA]	nicked DNA substrate, pH 7.5, 25-37°C, recombinant His-tagged wild-type enzyme	Homo sapiens